Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013372.1 Corchorus capsularis cultivar CVL-1 contig13393, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 23928
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:2696 original size:19 final size:19

Alignment explanation


    Indices: 2669--2708  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       2659 GGAAAAAAAA

                *         *    
       2669 ACCGTAACCGAAGCTACCG
          1 ACCGGAACCGAAGCAACCG

                       *       
       2688 ACCGGAACCGACGCAACCG
          1 ACCGGAACCGAAGCAACCG

              
       2707 AC
          1 AC

       2709 GTGCGTCGGC


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.33, C:0.40, G:0.23, T:0.05


Consensus pattern (19 bp):   
ACCGGAACCGAAGCAACCG

Found at i:2859 original size:2 final size:2

Alignment explanation


    Indices: 2852--2877  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       2842 TATTTTTAAT

                                                  
       2852 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

       2878 CACTATGTTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:23525 original size:26 final size:26

Alignment explanation


    Indices: 23496--23550  Score: 110
    Period size: 26  Copynumber: 2.1  Consensus size: 26

      23486 ATGTGTCTCC

                                      
      23496 AGTTGATGTCTCAAAAACAGTAATGA
          1 AGTTGATGTCTCAAAAACAGTAATGA

                                      
      23522 AGTTGATGTCTCAAAAACAGTAATGA
          1 AGTTGATGTCTCAAAAACAGTAATGA

               
      23548 AGT
          1 AGT

      23551 GTATGAATTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   29  1.00

ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27


Consensus pattern (26 bp):   
AGTTGATGTCTCAAAAACAGTAATGA

Found at i:23904 original size:2 final size:2

Alignment explanation


    Indices: 23892--23928  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      23882 AAATGTATGA

                  *                                                
      23892 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.